I've changed the version number and the build names so now for the
next version all goes with a different name, so I think that this
will allow different versions of libgepub running in the same system.
https://gitlab.gnome.org/GNOME/libgepub/commit/d721c7ebba040b935d3c8e
0456ccf5a4a674e531
These are all files that will install libgepub:
local
local/lib
local/lib/libgepub-0.6.so
local/lib/girepository-1.0
local/lib/girepository-1.0/Gepub-0.6.typelib
local/lib/libgepub-0.6.so.0.0.0
local/lib/libgepub-0.6.so.0
local/lib/pkgconfig
local/lib/pkgconfig/libgepub-0.6.pc
local/share
local/share/gir-1.0
local/share/gir-1.0/Gepub-0.6.gir
local/include
local/include/libgepub-0.6
local/include/libgepub-0.6/gepub-widget.h
local/include/libgepub-0.6/gepub-archive.h
local/include/libgepub-0.6/gepub-text-chunk.h
local/include/libgepub-0.6/gepub-doc.h
local/include/libgepub-0.6/gepub.h
With this change, anyone that uses libgepub should specify the
version in his code and link with -lgepub-0.6 for example.
Is this the recommended way to do that?

That looks correct, but I'm wondering which branches one is supposed to
use now. There's a libgepub-0.5 and a libgepub-0.6 branch, as well as a
master branch.
Usually, you'd use branches for continuing stable releases, and master
for ongoing development. Is libgepub-0.6 your tests before merging into
master?
Cheers